data_3E77 # _model_server_result.job_id ipQu0QpQoBM-WBXJPCTsSg _model_server_result.datetime_utc '2025-08-30 12:52:51' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3e77 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":400}' # _entry.id 3E77 # _exptl.entry_id 3E77 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 3E77 _cell.length_a 171 _cell.length_b 171 _cell.length_c 103.88 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3E77 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,D,E,F,G,H 1 1 C,I 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_555 -x,-x+y,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 34.626667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 F N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A NZ LYS 207 A LYS 200 1_555 D C4A PLP . A PLP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale2 B NZ LYS 207 B LYS 200 1_555 F C4A PLP . B PLP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? # _chem_comp.formula 'C8 H10 N O6 P' _chem_comp.formula_weight 247.142 _chem_comp.id PLP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN B6 Phosphate' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N1 C2 PLP doub 273 n y N1 C6 PLP sing 274 n y C2 C2A PLP sing 275 n n C2 C3 PLP sing 276 n y C2A H2A1 PLP sing 277 n n C2A H2A2 PLP sing 278 n n C2A H2A3 PLP sing 279 n n C3 O3 PLP sing 280 n n C3 C4 PLP doub 281 n y O3 HO3 PLP sing 282 n n C4 C4A PLP sing 283 n n C4 C5 PLP sing 284 n y C4A O4A PLP doub 285 n n C4A H4A PLP sing 286 n n C5 C6 PLP doub 287 n y C5 C5A PLP sing 288 n n C6 H6 PLP sing 289 n n C5A O4P PLP sing 290 n n C5A H5A1 PLP sing 291 n n C5A H5A2 PLP sing 292 n n O4P P PLP sing 293 n n P O1P PLP doub 294 n n P O2P PLP sing 295 n n P O3P PLP sing 296 n n O2P HOP2 PLP sing 297 n n O3P HOP3 PLP sing 298 n n # _atom_sites.entry_id 3E77 _atom_sites.fract_transf_matrix[1][1] 0.005848 _atom_sites.fract_transf_matrix[1][2] 0.003376 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006753 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009626 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code D 2 PLP A 1 400 400 PLP PLP . E 3 GOL A 1 500 500 GOL GOL . F 2 PLP B 1 400 400 PLP PLP . G 4 HOH A 1 501 1 HOH HOH . G 4 HOH A 2 502 2 HOH HOH . G 4 HOH A 3 503 3 HOH HOH . G 4 HOH A 4 504 6 HOH HOH . G 4 HOH A 5 505 7 HOH HOH . G 4 HOH A 6 506 9 HOH HOH . G 4 HOH A 7 507 11 HOH HOH . G 4 HOH A 8 508 12 HOH HOH . G 4 HOH A 9 509 15 HOH HOH . G 4 HOH A 10 510 18 HOH HOH . G 4 HOH A 11 511 20 HOH HOH . G 4 HOH A 12 512 23 HOH HOH . G 4 HOH A 13 513 25 HOH HOH . G 4 HOH A 14 514 27 HOH HOH . G 4 HOH A 15 515 33 HOH HOH . G 4 HOH A 16 516 34 HOH HOH . G 4 HOH A 17 517 44 HOH HOH . G 4 HOH A 18 518 45 HOH HOH . G 4 HOH A 19 519 46 HOH HOH . G 4 HOH A 20 520 49 HOH HOH . G 4 HOH A 21 521 51 HOH HOH . G 4 HOH A 22 522 56 HOH HOH . G 4 HOH A 23 523 58 HOH HOH . G 4 HOH A 24 524 59 HOH HOH . G 4 HOH A 25 525 62 HOH HOH . G 4 HOH A 26 526 63 HOH HOH . G 4 HOH A 27 527 69 HOH HOH . G 4 HOH A 28 528 71 HOH HOH . G 4 HOH A 29 529 73 HOH HOH . G 4 HOH A 30 530 80 HOH HOH . G 4 HOH A 31 531 82 HOH HOH . G 4 HOH A 32 532 84 HOH HOH . G 4 HOH A 33 533 85 HOH HOH . G 4 HOH A 34 534 86 HOH HOH . G 4 HOH A 35 535 87 HOH HOH . G 4 HOH A 36 536 90 HOH HOH . G 4 HOH A 37 537 95 HOH HOH . G 4 HOH A 38 538 96 HOH HOH . G 4 HOH A 39 539 97 HOH HOH . G 4 HOH A 40 540 103 HOH HOH . G 4 HOH A 41 541 107 HOH HOH . G 4 HOH A 42 542 108 HOH HOH . G 4 HOH A 43 543 113 HOH HOH . G 4 HOH A 44 544 114 HOH HOH . G 4 HOH A 45 545 122 HOH HOH . G 4 HOH A 46 546 123 HOH HOH . G 4 HOH A 47 547 125 HOH HOH . G 4 HOH A 48 548 128 HOH HOH . G 4 HOH A 49 549 130 HOH HOH . G 4 HOH A 50 550 131 HOH HOH . G 4 HOH A 51 551 134 HOH HOH . G 4 HOH A 52 552 135 HOH HOH . G 4 HOH A 53 553 137 HOH HOH . G 4 HOH A 54 554 139 HOH HOH . G 4 HOH A 55 555 142 HOH HOH . G 4 HOH A 56 556 143 HOH HOH . G 4 HOH A 57 557 146 HOH HOH . G 4 HOH A 58 558 152 HOH HOH . G 4 HOH A 59 559 153 HOH HOH . G 4 HOH A 60 560 155 HOH HOH . G 4 HOH A 61 561 156 HOH HOH . G 4 HOH A 62 562 158 HOH HOH . G 4 HOH A 63 563 159 HOH HOH . G 4 HOH A 64 564 160 HOH HOH . G 4 HOH A 65 565 161 HOH HOH . G 4 HOH A 66 566 163 HOH HOH . G 4 HOH A 67 567 164 HOH HOH . G 4 HOH A 68 568 183 HOH HOH . G 4 HOH A 69 569 185 HOH HOH . G 4 HOH A 70 570 188 HOH HOH . G 4 HOH A 71 571 192 HOH HOH . G 4 HOH A 72 572 195 HOH HOH . G 4 HOH A 73 573 202 HOH HOH . G 4 HOH A 74 574 210 HOH HOH . G 4 HOH A 75 575 213 HOH HOH . G 4 HOH A 76 576 231 HOH HOH . G 4 HOH A 77 577 244 HOH HOH . G 4 HOH A 78 578 252 HOH HOH . G 4 HOH A 79 579 263 HOH HOH . G 4 HOH A 80 580 267 HOH HOH . G 4 HOH A 81 581 268 HOH HOH . G 4 HOH A 82 582 269 HOH HOH . G 4 HOH A 83 583 283 HOH HOH . G 4 HOH A 84 584 289 HOH HOH . G 4 HOH A 85 585 294 HOH HOH . G 4 HOH A 86 586 298 HOH HOH . H 4 HOH B 1 401 4 HOH HOH . H 4 HOH B 2 402 10 HOH HOH . H 4 HOH B 3 403 13 HOH HOH . H 4 HOH B 4 404 14 HOH HOH . H 4 HOH B 5 405 26 HOH HOH . H 4 HOH B 6 406 28 HOH HOH . H 4 HOH B 7 407 32 HOH HOH . H 4 HOH B 8 408 38 HOH HOH . H 4 HOH B 9 409 42 HOH HOH . H 4 HOH B 10 410 48 HOH HOH . H 4 HOH B 11 411 52 HOH HOH . H 4 HOH B 12 412 57 HOH HOH . H 4 HOH B 13 413 65 HOH HOH . H 4 HOH B 14 414 67 HOH HOH . H 4 HOH B 15 415 68 HOH HOH . H 4 HOH B 16 416 70 HOH HOH . H 4 HOH B 17 417 72 HOH HOH . H 4 HOH B 18 418 77 HOH HOH . H 4 HOH B 19 419 79 HOH HOH . H 4 HOH B 20 420 81 HOH HOH . H 4 HOH B 21 421 89 HOH HOH . H 4 HOH B 22 422 91 HOH HOH . H 4 HOH B 23 423 98 HOH HOH . H 4 HOH B 24 424 101 HOH HOH . H 4 HOH B 25 425 102 HOH HOH . H 4 HOH B 26 426 124 HOH HOH . H 4 HOH B 27 427 127 HOH HOH . H 4 HOH B 28 428 129 HOH HOH . H 4 HOH B 29 429 136 HOH HOH . H 4 HOH B 30 430 140 HOH HOH . H 4 HOH B 31 431 168 HOH HOH . H 4 HOH B 32 432 172 HOH HOH . H 4 HOH B 33 433 177 HOH HOH . H 4 HOH B 34 434 178 HOH HOH . H 4 HOH B 35 435 181 HOH HOH . H 4 HOH B 36 436 193 HOH HOH . H 4 HOH B 37 437 197 HOH HOH . H 4 HOH B 38 438 198 HOH HOH . H 4 HOH B 39 439 206 HOH HOH . H 4 HOH B 40 440 209 HOH HOH . H 4 HOH B 41 441 216 HOH HOH . H 4 HOH B 42 442 220 HOH HOH . H 4 HOH B 43 443 222 HOH HOH . H 4 HOH B 44 444 229 HOH HOH . H 4 HOH B 45 445 248 HOH HOH . H 4 HOH B 46 446 249 HOH HOH . H 4 HOH B 47 447 259 HOH HOH . H 4 HOH B 48 448 272 HOH HOH . H 4 HOH B 49 449 284 HOH HOH . H 4 HOH B 50 450 293 HOH HOH . H 4 HOH B 51 451 297 HOH HOH . I 4 HOH C 1 371 8 HOH HOH . I 4 HOH C 2 372 17 HOH HOH . I 4 HOH C 3 373 19 HOH HOH . I 4 HOH C 4 374 22 HOH HOH . I 4 HOH C 5 375 29 HOH HOH . I 4 HOH C 6 376 31 HOH HOH . I 4 HOH C 7 377 37 HOH HOH . I 4 HOH C 8 378 40 HOH HOH . I 4 HOH C 9 379 47 HOH HOH . I 4 HOH C 10 380 50 HOH HOH . I 4 HOH C 11 381 53 HOH HOH . I 4 HOH C 12 382 64 HOH HOH . I 4 HOH C 13 383 88 HOH HOH . I 4 HOH C 14 384 100 HOH HOH . I 4 HOH C 15 385 105 HOH HOH . I 4 HOH C 16 386 117 HOH HOH . I 4 HOH C 17 387 141 HOH HOH . I 4 HOH C 18 388 166 HOH HOH . I 4 HOH C 19 389 167 HOH HOH . I 4 HOH C 20 390 169 HOH HOH . I 4 HOH C 21 391 175 HOH HOH . I 4 HOH C 22 392 187 HOH HOH . I 4 HOH C 23 393 214 HOH HOH . I 4 HOH C 24 394 221 HOH HOH . I 4 HOH C 25 395 240 HOH HOH . I 4 HOH C 26 396 241 HOH HOH . I 4 HOH C 27 397 247 HOH HOH . I 4 HOH C 28 398 261 HOH HOH . I 4 HOH C 29 399 291 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N1 PLP . . . D 2 68.635 -52.761 33.783 1 32.66 ? N1 PLP 400 A 1 HETATM 2 C C2 PLP . . . D 2 67.437 -52.127 33.975 1 33.31 ? C2 PLP 400 A 1 HETATM 3 C C2A PLP . . . D 2 67.449 -50.733 34.507 1 31.43 ? C2A PLP 400 A 1 HETATM 4 C C3 PLP . . . D 2 66.242 -52.787 33.665 1 35.95 ? C3 PLP 400 A 1 HETATM 5 O O3 PLP . . . D 2 65.036 -52.158 33.847 1 37.78 ? O3 PLP 400 A 1 HETATM 6 C C4 PLP . . . D 2 66.253 -54.094 33.161 1 36.44 ? C4 PLP 400 A 1 HETATM 7 C C4A PLP . . . D 2 65.02 -54.623 32.48 1 37.82 ? C4A PLP 400 A 1 HETATM 8 C C5 PLP . . . D 2 67.478 -54.735 32.973 1 36.43 ? C5 PLP 400 A 1 HETATM 9 C C6 PLP . . . D 2 68.659 -54.055 33.287 1 35.29 ? C6 PLP 400 A 1 HETATM 10 C C5A PLP . . . D 2 67.551 -56.156 32.443 1 36.44 ? C5A PLP 400 A 1 HETATM 11 O O4P PLP . . . D 2 67.251 -56.234 31.061 1 35.75 ? O4P PLP 400 A 1 HETATM 12 P P PLP . . . D 2 67.179 -57.681 30.358 1 34.11 ? P PLP 400 A 1 HETATM 13 O O1P PLP . . . D 2 68.453 -58.469 30.579 1 34.17 ? O1P PLP 400 A 1 HETATM 14 O O2P PLP . . . D 2 66.927 -57.472 28.891 1 34.04 ? O2P PLP 400 A 1 HETATM 15 O O3P PLP . . . D 2 66.023 -58.446 30.967 1 37.02 ? O3P PLP 400 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #